seqinr (version 3.4-5)

plotabif: Electrophoregram plot for ABIF data

Description

Simple chromatogram plot for data imported with the read.abif function.

Usage

plotabif(abifdata, 
  chanel = 1, 
  tmin = 1/tscale, 
  tmax = abifdata$Data[["SCAN.1"]]/tscale, 
  tscale = 1000, 
  yscale = 1000, type = "l", las = 1, 
  xlab = paste("Time", tscale, sep = "/"),
  ylab = paste("RFU", yscale, sep = "/"), 
  irange = (tmin*tscale):(tmax*tscale),
  x = irange/tscale,
  xlim = c(tmin, tmax),
  chanel.names = c(1:4,105),
  DATA = paste("DATA", chanel.names[chanel], sep = "."),
  y = abifdata$Data[[DATA]][irange]/yscale,
  ylim = c(min(y), max(y)),
  dyn = abifdata$Data[[paste("DyeN", chanel, sep = ".")]],
  main = paste(deparse(substitute(abifdata)), chanel, dyn, sep = " ; "),
  calibr = NULL,
  ladder.bp = NULL,
  allele.names = "identifiler",
  ladder.lab = TRUE,
  ...)

Arguments

abifdata

the result returned by read.abif

chanel

the dye number

tmin

scaled starting time for the time axis

tmax

scaled ending time for the time axis

tscale

scale factor for the time axis

yscale

scale factor for the y-axis (RFU)

type

type of line drawing forwarded to plot

las

orientation of axis labels forwarded to plot

xlab

x-axis label forwarded to plot

ylab

y-axis label forwarded to plot

irange

indices of data to be plotted

x

values used for the x-axis

xlim

limits for the x-axis forwarded to plot

chanel.names

numbers extensions used for the DATA

DATA

names of the DATA components

y

values used for the y-axis

ylim

limits for the y-axis forwarded to plot

dyn

dye name

main

title for the plot forwarded to plot

calibr

an optional calibration function to convert time into bp

ladder.bp

an optional ladder scale in bp (calibr must be provided)

allele.names

name of the dataset with allele names

ladder.lab

logical: should allele names be added on plot

...

arguments forwarded to plot

Value

Returns invisibly its local graphical parameter settings.

References

citation("seqinr")

See Also

function read.abif to import files in ABIF format, data gs500liz for internal size standards, data identifiler for allele names in the allelic ladder, data JLO for an example of an individual sample file, data ECH for an example of an allelic lader.

Examples

# NOT RUN {
data(ECH)
plotabif(ECH,chanel = 1, tmin = 3.2, tmax = 6.1)
# }